Jason wrote: <snip> I propose that we adopt a new value for PDB files :) The D-value (density) which is a measure of the <D/sigD> for each atom. Thus, when a PBD file is deposited, depositors can be asked to justify/explain the reason for including atoms with values less than a cutoff (0.5?) with an option to automatically remove them and re-refine the structure with the atoms removed. <snip> OK, but in what respect is this different to the B-value column in terms of novice users ignoring it? You can also truncate the model with a B-value cut off, no need to change the PDB format (which is obsolete anyway, but that is a different discussion :) Flip
_____ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jason Greenwald Sent: Wednesday, January 10, 2007 14:27 To: ccp4BB Subject: Re: Fwd: [ccp4bb]: Modelling disordered side-chains David Briggs wrote: > I always leave these atoms in, in a preferred rotamer (with > 1.0 occupancy!) and let the B-values refine to >100. These high B-values > clearly indicate the issue at hand, and you can colour the model > accordingly. ...assuming the end-user knows what a B-factor is... If you can't say with certainty that it's there... why detract from the accuracy of your model by including stuff that isn't in the data. you are artificially increasing the R-factor of your model by making your obs:param ratio less favourable. I personally exclude atoms from the model that are not visible in the electron density.... with the caveat that I use my judgment (as we all do) when it comes to "visible". However, if the B-factor is ignored by end-users, then leaving out side chains that have a large degree of mobility in the structure will not make end-user's calculations any more accurate (and will be less accurate if they model an interaction with a beta-carbon-truncated LYS in place of an entire LYS). It would obviously help if the software gives warnings about unusual features in the PBD for novice users. I propose that we adopt a new value for PDB files :) The D-value (density) which is a measure of the <D/sigD> for each atom. Thus, when a PBD file is deposited, depositors can be asked to justify/explain the reason for including atoms with values less than a cutoff (0.5?) with an option to automatically remove them and re-refine the structure with the atoms removed. Seriously though, if this (simple?) feature were to be built-in to refinement software I think that it would be easier for a large community to reach an agreement on how to represent disorder in atomic models. -- Jason Greenwald UPR9050 CNRS Pole API - ESBS Bd Sebastien Brandt BP 10413 67412 Illkirch Cedex France Tel 33 (0)3 90 24 47 31 Fax 33 (0)3 90 24 48 29 [EMAIL PROTECTED] http://recepteurs.u-strasbg.fr
